Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences - PubMed (original) (raw)

Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences

Derrick E Fouts. Nucleic Acids Res. 2006.

Abstract

Phage_Finder, a heuristic computer program, was created to identify prophage regions in completed bacterial genomes. Using a test dataset of 42 bacterial genomes whose prophages have been manually identified, Phage_Finder found 91% of the regions, resulting in 7% false positive and 9% false negative prophages. A search of 302 complete bacterial genomes predicted 403 putative prophage regions, accounting for 2.7% of the total bacterial DNA. Analysis of the 285 putative attachment sites revealed tRNAs are targets for integration slightly more frequently (33%) than intergenic (31%) or intragenic (28%) regions, while tmRNAs were targeted in 8% of the regions. The most popular tRNA targets were Arg, Leu, Ser and Thr. Mapping of the insertion point on a consensus tRNA molecule revealed novel insertion points on the 5' side of the D loop, the 3' side of the anticodon loop and the anticodon. A novel method of constructing phylogenetic trees of phages and prophages was developed based on the mean of the BLAST score ratio (BSR) of the phage/prophage proteomes. This method verified many known bacteriophage groups, making this a useful tool for predicting the relationships of prophages from bacterial genomes.

PubMed Disclaimer

Figures

Figure 1

Figure 1

Flow chart of Phage_Finder pipeline (A) and Phage_Finder.pl script (B) logic. Standard symbols for constructing flow charts were used.

Figure 2

Figure 2

Predicted prophage target-site distributions. The distribution of targets where Phage_Finder found putative attachment sites (A). The genetic code table indicates the distribution of tRNA targets (B). For each codon, the number of phages from Williams, 2002 and the number of predicted prophages from this study are indicated, separated by a colon. The gray-highlighted numbers demarcate those codons that are targeted six or more times. The point of insertion on a consensus tRNA molecule was mapped (C) for Phage_Finder predicted prophages (upper), phages and prophages from the literature [(27), middle] and the two datasets combined (lower). The arrows point to the nucleotide insertion point while the numbers indicate number of insertions at each insertion point. Red arrows and numbers in the combined dataset show those locations that are unique to either dataset, while gold colored arrows and numbers highlight common insertion points between the two datasets. The frequency and position of insertion into a consensus tRNA gene is noted in (D). Red bars indicate _Phage_Finder_-predicted insertion events while green bars represent insertion events reported from the literature (27).

Figure 3

Figure 3

Test phylogenetic tree generated by converting the BSR of BLASTP bidirectional matches into distance (A). Whole genome BLASTP data from Fouts et al., 2005 (37) was used to compute this tree. The previously published 16S rRNA tree (B) is shown for comparison.

Figure 4

Figure 4

Phylogenetic analysis of Phage_Finder predicted prophages, known prophages and sequenced phage genomes. The radial tree was constructed with branch length extensions. The branches were colored as follows: sequenced phage genomes (black), known prophages (blue), Phage_Finder predicted prophage regions (gold). Only key phages or prophages are noted for clarity. Known phage groups are indicated in red.

Similar articles

Cited by

References

    1. Sullivan M.B., Waterbury J.B., Chisholm S.W. Cyanophages infecting the oceanic cyanobacterium Prochlorococcus. Nature. 2003;424:1047–1051. - PubMed
    1. Mann N.H., Cook A., Millard A., Bailey S., Clokie M. Bacterial photosynthesis genes in a virus. Nature. 2003;424:741. - PubMed
    1. Wagner P.L., Waldor M.K. Bacteriophage control of bacterial virulence. Infect. Immun. 2002;70:3985–3993. - PMC - PubMed
    1. Schuch R., Fischetti V.A. Detailed genomic analysis of the Wbeta and Gamma phages infecting Bacillus anthracis: implications for evolution of environmental fitness and antibiotic resistance. J. Bacteriol. 2006;188:3037–3051. - PMC - PubMed
    1. Stone R. Bacteriophage therapy. Stalin's forgotten cure. Science. 2002;298:728–731. - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources